Both myocardial infarction and ischemic stroke are rare in the young. Yet a 15-year-old male patient suffered a myocardial infarction and later an ischemic stroke despite uninterrupted antiplatelet therapy. His medical history involved the surgical correction of an incomplete atrioventricular canal defect at the age of 13 years. No cardiovascular risk factors other than elevated lipoprotein(a) level could be identified. His antithrombin (AT) activity was decreased and DNA sequence analysis revealed heterozygosity for AT Basel (p.Pro41Leu), a variant with impaired heparin binding. This report supports a possible additional pathophysiological role for AT Basel and elevated lipoprotein(a) level in arterial thrombogenesis.